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gnu: Add r-bsgenome-mmusculus-ucsc-mm10.

Message ID 20160614125030.13866-1-ricardo.wurmus@mdc-berlin.de
State New
Headers show

Commit Message

Ricardo Wurmus June 14, 2016, 12:50 p.m. UTC
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
  variable.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

Comments

Andreas Enge June 15, 2016, 1:59 p.m. UTC | #1
Hello Ricardo,

On Tue, Jun 14, 2016 at 02:50:30PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
>   variable.

this looks safe to push.

Andreas
Ricardo Wurmus June 15, 2016, 3:07 p.m. UTC | #2
Andreas Enge <andreas@enge.fr> writes:

> Hello Ricardo,
>
> On Tue, Jun 14, 2016 at 02:50:30PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
>>   variable.
>
> this looks safe to push.

Thanks.  Pushing to master now.

~~ Ricardo
diff mbox

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 753e657..0b6698f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5245,6 +5245,38 @@  by UCSC (hg19, February 2009) and stored in Biostrings objects.")
 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-mmusculus-ucsc-mm10
+  (package
+    (name "r-bsgenome-mmusculus-ucsc-mm10")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "BSgenome.Mmusculus.UCSC.mm10_"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
+    (properties
+     `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)))
+    (home-page
+     "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
+    (synopsis "Full genome sequences for Mouse")
+    (description
+     "This package provides full genome sequences for Mus
+musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
+in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")